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Synthesis, growth, molecular structure and spectral studies of 1,3 diglycinyl thiourea by density functional method
Optik 126 (2015) 1117–1122
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Optik journal homepage: www.elsevier.de/ijleo
Synthesis, growth, molecular structure and spectral studies of 1,3 diglycinyl thiourea by density functional method M. Kumar a , R. Kanagadurai b , G. Mani a , S. Gunasekaran c , S. Kumaresan a,∗ a b c
PG and Research Department of Physics, Arignar Anna Government Arts College, Cheyyar 604 407, India PG and Research Department of Physics, Presidency College, Chennai 600 005, India St. Peter’s University, Avadi, Chennai 600 109, India
a r t i c l e
i n f o
Article history: Received 19 February 2014 Accepted 4 March 2015 Keywords: 1,3 Diglycinyl thiourea Hydrogen bonding FTIR UV DFT
a b s t r a c t Glycine is an important amino acid for building up protein synthesis and thiourea – a matrix metal multiplier combines to form a hybrid single crystal. Crystals of 1,3 diglycinyl thiourea were grown from aqueous solution by slow evaporation method. Powder X-ray diffraction analysis confirms that 1,3 diglycinyl thiourea crystallizes to monoclinic system. It is predicted that the molecular structure of 1,3 diglycinyl thiourea having well-defined bonding between C O. . .H and N H. . .O bond with a distance of 1.946 A˚ through hydrogen bonding. The structure and spectroscopic data of the molecule in the ground state have been calculated using ab initio Hartree Fock (HF) and density functional theory (DFT) (B3LYP) methods by employing 6-31 G(d,p) basis sets. Optical absorption study reveals that the transparency of the crystal in the entire visible region and the cutoff wavelength was found to be 236 nm. Mullikan population analyses on atomic charges analysis and molecular electrostatic potential and total density distribution are constructed to understand the electronic properties. The detailed interpretation of the vibrational spectra has been made on the basis of normal coordinate analysis. It is reported that there is a good agreement between theoretical and observed values. © 2015 Elsevier GmbH. All rights reserved.
1. Introduction The need for materials which combine large non linear optical characteristics with resistance to physical and chemical attack and good growth properties has led to the investigation of the semi organic materials. Semi organics are formed by combining organic molecules of high polarizability with mechanically strong and thermally stable inorganic molecules. The search for novel materials gaining increased attention in recent years and a wide variety of both organic and inorganic materials has been developed. Problems with both classes of materials have resulted in the investigation of semi organics [1–6]. The semi organic materials have the potentials for combining the high optical non linearity and chemical flexibility of organics with thermal stabilities and excellent transmittance of inorganic [7,8]. In search of these semi organic materials, urea and urea analogs have been explored [9]. 1,3 Diglycinyl thiourea single crystals were grown and characterized by XRD, optical and thermal properties were reported [10]. However, the detailed ab initio HF and B3LYP comparative studies on the complete FTIR spectrum and UV–vis spectrum of 1,3 diglycinyl thiourea have not
∗ Corresponding author. Tel.: +91 4182 22 5313. E-mail address: [email protected] (S. Kumaresan). http://dx.doi.org/10.1016/j.ijleo.2015.03.019 0030-4026/© 2015 Elsevier GmbH. All rights reserved.
been reported so far. Therefore, in the present study, molecular geometry, optimized parameters and vibrational frequencies are computed and the performances of the computational methods for HF and DFT (B3LYP) levels at 6-31 G(d,p) basis sets is compared. In this study, density functional theory (DFT/B3LYP) and by using hybrid functional, ab initio Hartree–Fock (HF) computations of the vibrational spectrum, the molecular geometry, and atomic charges calculations were carried out for 1,3 diglycinyl thiourea molecule. The experimental geometric data of the molecule were taken from the Cambridge crystallographic database [11]. The entire calculations were performed using ab initio HF and density functional theory (DFT) to support our wave number assignment. Density functional calculations are reported to provide excellent vibrational wave number of organic compounds if the calculated frequencies are scaled to compensate for the approximate treatment of electron correlation for basis set deficiencies and for the anharmonicity. 2. Experimental 2.1. Synthesis Glycine (AR) grade and thiourea (AR) were taken in the ratio 2:1 in distilled water and stirred in a magnetic stirrer for 6 h at room temperature. The solution was heated in steps of 5 ◦ C and
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M. Kumar et al. / Optik 126 (2015) 1117–1122 55 Glycine 50
Thiourea
Concentraon (gm/100ml)
1,3 diglycinyl thiourea 45
40
35
30
25
20 25
30
35
40
45
50
55
Temperatureºc
Fig. 1. Solubility curves for glycine, thiourea and 1,3 diglycinyl thiourea.
the precipitates if any to get dissolved. The solution is filtered and refluxed for homogeneity and purity. The obtained product is 1,3 diglycinyl thiourea.
Fig. 2. Photograph of a grown 1,3 diglycinyl thiourea single crystal.
2(NH2 CH2 COOH) + CS(NH2 )2 → C5 H10 N4 O2 S 2.2. Solubility test Solubility of 1,3 diglycinyl thiourea has been determined for five different temperatures at 30 ◦ C, 35 ◦ C, 40 ◦ C, 45 ◦ C and 50 ◦ C. Re-crystallized salt is used for this purpose. A 250 ml glass beaker containing 100 ml of deionized water was placed in the temperature bath. The initial temperature of the bath was set at 30 ◦ C. The beaker was closed with a sheet and placed in the magnetic stirrer. The synthesized salt was added in small amount and the stirring of the solution was continued till the formation of precipitate, which confirmed the saturation of the solution. The stirring further confirmed to have uniform temperature and concentration throughout the entire volume of the solution. On reaching the saturation, the equilibrium concentration of the solution was analyzed gravimetrically. The same procedure was followed for glycine and thiourea. Fig. 1 shows the solubility curves of glycine, thiourea and 1,3 diglycinyl thiourea. 2.3. Growth of 1,3 diglycinyl thiourea single crystals Single crystals of 1,3 diglycinyl thiourea were grown by slow evaporation technique at room temperature. Saturated solutions were prepared using re-crystallized salt at room temperature. The solutions were filtered using filter paper and kept undisturbed at room temperature and allow evaporating the solvent by covering a perforated thin mica sheet over the beaker. Transparent and optically good quality seeds were selected for the growth experiments. The period of growth ranged between 3 and 4 weeks and the harvested crystals are characterized. The photograph of optically transparent 1,3 diglycinyl thiourea single crystals are shown in Fig. 2.
Fig. 3. The optimized structure of 1,3 diglycinyl thiourea at DFT/6-31 G(d,p).
vibrational frequency calculations at the HF and DFT levels to characterize all stationary points as minima. The ground state optimized structural parameters such as bond length, bond angle and dihedral angle in various basis sets are presented in Table 1. From the theoretical values, it is found that some of the calculated parameters are slightly deviated from the experimental values, due to the fact that theoretical calculations belong to molecule in the gaseous phase and the experimental results belong to molecule in solid state. In this work, we performed full geometry optimization of the title compound. The optimized structure of title compound at DFT is shown in Fig. 3. The B3LYP method leads to geometry parameters, which are close to experimental data. A statistical treatment of these data shows that for the bond lengths B3LYP/631 G(d,p) are slightly better than the HF/6-31 G(d,p) geometry. The slight variation with the experimental value is due to the fact that the optimization performed in an isolated condition, whereas the experimental environment affected the X-ray structure.
3. Theoretical methods 3.2. Vibrational spectra 3.1. Molecular geometry The entire calculations were performed at ab initio HF and DFT (B3LYP) levels at 6-31 G(d,p) basis sets on a Pentium V/1.6 GHz personal computer using Gaussian 03W program package [12] and applying geometry optimization [13]. Initial geometry generated was minimized at the Hartree–Fock levels using 6-31 G(d,p) basis set and again re-optimized at DFT (B3LYP) levels at 6-31 G(d,p) basis sets. The optimized structural parameters were used in the
The present molecule has C1 symmetry and has 60 normal modes of vibrations; all the fundamental modes are active in infrared. None of the predicted vibrational spectra have any imaginary frequency, implying that the optimized geometry is located at the local lowest point on the potential energy surface. We know that, ab initio Hartree–Fock and DFT potentials systematically overestimate the vibrational wave numbers. These discrepancies corrected wither by computing harmonic corrections explicitly or
M. Kumar et al. / Optik 126 (2015) 1117–1122
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Table 1 Optimized geometric parameters of 1,3 diglycinyl thiourea at HF and DFT (B3LYP) levels of 6-31 G (d,p) basis sets. Theoretical
Experimental
HF/6-31 G(d,p) R(1-2) R(1-9) R(1-13) R(2-3) R(2-4) R(4-5) R(4-14) R(5-7) R(5-8) R(6-7) R(6-15) R(6-16) R(7-17) R(7-18) R(9-11) R(9-12) R(10-11) R(10-19) R(10-20) R(11-21) R(11-22) R(12-14)
B3LYP/6-31 G(d,p) 1.39 1.37 1 1.71 1.35 1.39 1.01 1.52 1.21 1.44 0.99 0.99 1.08 1.08 1.51 1.22 1.43 0.99 0.99 1.08 1.09 1.95
A(2-1-9) A(2-1-13) A(1-2-3) A(1-2-4) A(9-1-13) A(1-9-11) A(1-9-12) A(3-2-4) A(2-4-5) A(2-4-14) A(5-4-14) A(4-5-7) A(4-5-8) A(4-14-12) A(7-5-8) A(5-7-6) A(5-7-17) A(5-7-18) A(7-6-15) A(7-6-16) A(6-7-17) A(6-7-18) A(15-6-16) A(17-7-18) A(11-9-12) A(9-11-10) A(9-11-21) A(9-11-22) A(9-12-14) A(11-10-19) A(11-10-20) A(10-11-21) A(10-11-22) A(19-10-20) A(21-11-22)
130.86 111.77 116.4 115.37 117.38 114.63 123.33 128.22 128.77 118.4 112.83 113.87 126.05 131.66 120.08 114.52 106.26 106.21 118.76 118.76 111.54 111.6 114.65 106.18 121.99 109.81 109.35 106.24 100.32 117.62 116.82 110.04 114.38 116.3 106.86
R(1-2) R(1-9) R(1-13) R(2-3) R(2-4) R(4-5) R(4-14) R(5-7) R(5-8) R(6-7) R(6-15) R(6-16) R(7-17) R(7-18) R(9-11) R(9-12) R(10-11) R(10-19) R(10-20) R(11-21) R(11-22) R(12-14)
1.411 1.383 1.014 1.709 1.366 1.401 1.035 1.54 1.235 1.451 1.008 1.008 1.097 1.097 1.524 1.251 1.442 1.007 1.01 1.102 1.109 1.946
by introducing a scaled field or directly scaling the calculated wave number with the proper factor. The DFT method is superior to HF and semi-empirical methods in terms of realistic reproduction of both band intensity distribution and general spectral features.
X-ray data/ref. [11] A(2-1-9) A(2-1-13) A(1-2-3) A(1-2-4) A(9-1-13) A(1-9-11) A(1-9-12) A(3-2-4) A(2-4-5) A(2-4-14) A(5-4-14) A(4-5-7) A(4-5-8) A(4-14-12) A(7-5-8) A(5-7-6) A(5-7-17) A(5-7-18) A(7-6-15) A(7-6-16) A(6-7-17) A(6-7-18) A(15-6-16) A(17-7-18) A(11-9-12) A(9-11-10) A(9-11-21) A(9-11-22) A(9-12-14) A(11-10-19) A(11-10-20) A(10-11-21) A(10-11-22) A(19-10-20) A(21-11-22)
130.5 111.5 116.9 114.9 117.9 114.6 123.5 128.2 128.4 119.4 112.2 112.2 126.6 130.8 121.2 114.1 106.4 106.4 118.3 118.2 111.6 111.9 114.2 106 121.8 109.6 108.5 106.4 100.8 117.7 115.1 111.8 114.2 116.3 106
R(1-2) R(1-9) R(1-13) R(2-3) R(2-4) R(4-5) R(4-14) R(5-7) R(5-8) R(6-7) R(6-15) R(6-16) R(7-17) R(7-18) R(9-11) R(9-12) R(10-11) R(10-19) R(10-20) R(11-21) R(11-22)
1.369 1.369 1.012 1.576 1.369 1.369 1.012 1.509 1.208 1.468 1.02 1.02 1.113 1.113 1.509 1.208 1.468 1.02 1.02 1.113 1.113
A(2-1-9) A(2-1-13) A(1-2-3) A(1-2-4) A(9-1-13) A(1-9-11) A(1-9-12) A(3-2-4) A(2-4-5) A(2-4-14) A(5-4-14) A(4-5-7) A(4-5-8)
125.1 117.5 124.3 120 117.5 114.3 122.9 115.7 125.1 117.5 117.5 114.3 122.9
A(7-5-8) A(5-7-6) A(5-7-17) A(5-7-18) A(7-6-15) A(7-6-16) A(6-7-17) A(6-7-18) A(15-6-16) A(17-7-18) A(11-9-12) A(9-11-10) A(9-11-21) A(9-11-22)
122.8 110.7 108.8 108.8 109.5 109.5 108.8 108.8 104.5 110.9 122.8 110.7 108.8 108.8
A(11-10-19) A(11-10-20) A(10-11-21) A(10-11-22) A(19-10-20) A(21-11-22)
109.5 109.5 108.8 108.8 104.5 110.9
revealed that 1,3 diglycinyl thiourea crystal belongs to monoclinic crystal system. The obtained crystallographic data are presented in Table 2. 4.2. Optical absorption studies
4. Results and discussion 4.1. X-ray diffraction analysis The scheme of the crystal data from the Cambridge crystal data were presented in Table 2. From the table, it is observed that the ˚ c = 12.273 A˚ and cell parameters are a = 5.5753 A˚ and b = 5.994 A, V = 310.81 A˚ 3 . The crystals that belong to the monoclinic crystal system are in good agreement with the reported data [10] and are indexed. X-ray diffraction analysis was done using diffractometer model Philips Powder X-ray diffractometer using CuK␣ ˚ and is shown in Fig. 4. The samples were scanned ( = 1.5418 A) over the range 20–60◦ at a scan rate of 1◦ /min. The unit cell dimensions were calculated using PROSZKI software package. The study
The optical absorption spectrum of 1,3 diglycinyl thiourea single crystal was recorded in the range 200–800 nm using a Varian Cary 5E model spectrophotometer and is shown in Fig. 5. The spectrum shows that 1,3 diglycinyl thiourea crystal has good transmission in the entire region. The lower cutoff wavelength lies below 236 nm, whereas the calculated cutoff wavelength is at 258 nm at TD DFT/6-31 G(d,p) basis set. The overestimation of value in the theoretical spectra is due to anharmonicity in the real system. Efficient
Table 2 Crystal data of 1,3 diglycinyl thiourea single crystal. Crystallographic data
1,3 Diglycinyl thiourea
˚ a (A) ˚ b (A) ˚ c (A)
5.5753 5.994 12.273 310.81 90◦ 113◦ 90◦ Monoclinic
Volume (A˚ 3 ) ˛ ˇ Crystal system
Fig. 4. Powder XRD pattern of 1,3 diglycinyl thiourea.
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M. Kumar et al. / Optik 126 (2015) 1117–1122
236 nm, 1.267
1.2
Experimental
1.0 0.8 0.6
Absorbance
0.4 0.2 0.0 2.0
TD DFT/6-31G(d,p)
258 nm, 2.101
1.5
1.0
0.5
0.0
200
400
600
800
Wavelength (nm)
Fig. 7. The contour map of molecular electrostatic potential surface of 1,3 diglycinyl thiourea.
Fig. 5. The optical absorption spectrum of DGT crystal.
NLO crystals have an optical transparency lower cutoff wavelength between 200 and 400 nm [14]. From the UV–vis spectral analysis it is clear that the cut off wavelength is at 236 nm and there is no significant absorption in the UV region thereby confirming the advantages of the crystals, the large transmission in the entire region and short cutoff wavelength enable the crystals to be useful for second harmonic generation. The percentage of absorption of 1,3 diglycinyl thiourea crystals is more than one, indicating that these crystals have good optical property. 4.3. FTIR studies 1,3 Diglycinyl thiourea single crystal was subjected to the FTIR studies. The various functional groups present in 1,3 diglycinyl thiourea crystals were identified and confirmed by the FTIR study. The complete vibrational assignments of fundamental modes of 1,3 diglycinyl thiourea are presented in Table 3. The spectrum was recorded in the range 4000–400 cm−1 using BRUKER IFS – 66V spectrometer, by KBr pellet technique and is shown in Fig. 6.
DFT/6-31 G(d,p)
4.4. Vibrational assignments A medium sharp band at 1721 cm−1 is due to NH2 scissoring and the scaled value of 1722 in B3LYP/6-31 G(d,p) is assigned. A weak peak at 3441 cm−1 is assigned to NH2 asymmetric stretching and calculated the values at 3431 and 3450 in HF and DFT methods, respectively. The CN asymmetric and symmetric stretching vibrations are observed at 1089 and 1472 cm−1 , respectively. The CS asymmetric stretching vibration is observed at 1408 cm−1 . Thiourea could form metal complexes by coordinate bonds through sulfur or nitrogen. Thiourea exhibits characteristic peaks at 1627, 1472, 1417, 1089, 740 and 494 cm−1 [15]. The CS symmetric stretching is observed at 740 cm−1 . The band at 494 cm−1 is due to asymmetric NCN bending. If the bonding is through sulfur, there will be a decrease in the CS stretching frequency and an increase in the CN stretching frequency. The reverse happens if it is through nitrogen. The peak set around 921 and 894 cm−1 could be attributed to CH2 wagging and CNH and CNC out of plane banding. A peptide bond CO NH that is formed between the NH2 in glycine and thiourea is clearly visible in the spectrum between 1030 and 1750 cm−1 [16,17]. Also the C O and N H stretching vibrations of CO NH are visible at 2686 cm−1 and 2706 cm−1 in the stimulated spectra, whereas both the peaks absent in the experimental spectrum. The broad envelope positioned between 2750 and 3500 cm−1 corresponds to the symmetric and asymmetric stretching modes of NH2 group [18].
Transmittance (T%)
4.5. Molecular electrostatic potential mapping (MESP) studies Molecular electrostatic potential mapping helps to a larger extent in investigating the structure and the charge distribution of molecules three dimensionally with its physiochemical properties. The molecular electrostatic potential (MESP) of 1.3 diglycinyl thiourea is carried out using DFT/B3LYP/6-31 G(d,p) method and it visibly suggests that the hydrogen atoms attached to the ends of the molecular chain beat the maximum bang of positive charge [19]. The molecular electrostatic potential surface (MESP) provides a visual method to understand the polarity of the molecule. The purpose of finding the electrostatic potential is to find the reactive site of a molecule. The MESP mapped surface of the compound is shown in Fig. 7 and computed at 0.004 at iso-density surface.
HF/6-31 G(d,p)
Expe rimen tal
4000
3000
2000
1000
0
4.6. Mulliken charges
-1
Wavenu mber (cm ) Fig. 6. FTIR spectra of 1,3 diglycinyl thiourea.
The calculation of effective atomic charges plays an important role in the application of quantum mechanical calculations to
M. Kumar et al. / Optik 126 (2015) 1117–1122
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Table 3 Observed FTIR and calculated wave number for 1,3 diglycinyl thiourea using HF 6-31 G(d,p) and DFT/B3LYP G(d,p) methods. Theoretical
Experimental
B3LYP/6-31 G(d,p)
HF/6-31 G(d,p)
Unscaled
Scaled
IR intensity
Unscaled
Scaled
IR intensity
30 43 49 69 101 103 156 178 185 226 271 280 325 384 451 481 523 545 547 589 658 668 704 788 795 908 931 996 1038 1077 1117 1132 1161 1184 1193 1236 1254 1261 1362 1368 1397 1443 1502 1547 1554 1572 1664 1710 1719 1747 2920 2998 3057 3102 3239 3585 3596 3609 3726 3730
29 41 47 66 97 99 150 171 177 217 260 269 312 369 433 462 502 523 525 565 632 641 676 756 763 872 894 957 997 1034 1073 1087 1115 1137 1145 1187 1204 1210 1308 1313 1342 1385 1442 1486 1492 1509 1598 1642 1650 1677 2686 2758 2812 2854 2980 3298 3308 3320 3428 3431
1.38 4.20 1.86 10.41 3.94 9.61 30.28 10.59 4.14 3.02 4.22 1.46 26.99 13.73 98.65 217.00 243.99 46.41 46.11 29.66 7.83 46.64 12.47 103.04 35.38 7.12 20.77 12.94 1.50 126.53 15.56 36.07 105.27 4.84 57.01 76.31 68.31 82.80 342.25 5.88 95.50 61.59 6.90 526.07 244.42 568.00 144.62 46.09 41.18 81.68 61.58 44.60 18.47 8.70 302.49 28.00 16.00 11.44 17.47 20.80
27 40 58 69 108 125 184 203 212 246 281 305 351 405 487 537 578 587 604 643 717 724 766 835 891 985 1009 1078 1127 1154 1205 1211 1265 1291 1302 1342 1380 1397 1477 1488 1529 1592 1624 1666 1718 1768 1817 1845 1893 1936 3111 3223 3229 3270 3632 3833 3840 3852 3963 3966
26 38 55 66 103 120 176 195 204 236 269 293 337 389 467 515 555 564 580 617 688 695 735 802 856 946 968 1035 1082 1108 1157 1162 1214 1239 1250 1288 1325 1341 1418 1428 1468 1528 1559 1600 1649 1654 1659 1679 1722 1762 2706 2804 2810 2845 3160 3335 3341 3351 3447 3450
1.10 4.43 2.07 13.08 5.72 4.11 20.80 3.20 50.65 2.33 4.20 0.42 13.65 13.32 40.54 306.54 273.81 127.98 31.26 35.46 34.52 60.71 65.06 41.13 141.13 1.89 11.65 7.31 10.05 221.71 52.03 14.75 85.51 199.85 8.91 88.23 249.60 42.80 560.27 3.64 52.87 31.35 3.43 13.70 598.34 758.53 75.95 64.64 150.22 125.65 49.52 15.65 25.62 8.14 305.07 15.36 20.98 65.78 32.93 33.30
Vibrational assignment
FTIR
Intensity
Wave number (cm−1 )
%
509
82
673 731
91 84
894 921
79 96
1030
97
1111
95
1328 1408 1433 1483
75 64 94 80
1618
48
1721
3213
48
3441
27
Lattice vibrations Lattice vibrations Lattice vibrations Lattice vibrations Lattice distortion Lattice distortion W(NH2 + C NH2 ) W(NH2 + C CH2 ) W(NH2 + C NH2 ) Lattice distortion D(C NH2 ) Lattice twist Lattice twist (CO· · ·H + NH· · ·O) (CO· · ·H) + (CCH) (CO· · ·H + CNC) (C NH2 ) (C NH2 ) (C NH2 ) + (C CH2 ) Lattice breath (C NH2 ) + (C NH· · ·O) (CS) + (C NH· · ·O) + ␥(CNH) (C CH2 + C NH2 ) + ␥(CCO + NCO) (CS) + W(CH2 ) + ␥(CNC + CNH) (C NH· · ·O) ␥(C NH2 ) + (CNH) + (CH2 ) W(CH2 ) + ␥(CNC + CNH) ␥(CNC + CNH + NCO) ␥(CCO + NHO) ␥(NH· · ·O + CO· · ·H) ␥(CNC + CNH + CO· · ·H) ␥(C NH2 ) + (CNH) ␥(C NH2 ) + (CNH) W(NH2 + CH2 ) W(CH2 ) + ␥(CNC + CNH) ␥(CNC + CNH + NCO) ␥(CNC + CNH + NCO) (C CH2 + C NH2 + CCO + NCO) (CH2 ) + (CNH) (CNC + CNH + NCO + NH· · ·O) (CH2 + NH2 ) cradle a (CS) + (CH2 ) (C CH2 ) + NH2 cradle CH2 scissoring (C CH2 + CNH + NHO) (C CH2 + CNH + COH + NHO) (COH + NHO) NH2 scissoring NH2 scissoring (CO) + (NH2 ) + (COH) + (CC NH2 ) (CO) + (NH2 ) + (COH) (CH) (CH) s (CH2 ) a (CH2 ) (NH) s (NH2 ) s (NH2 ) a (NH2 ) a (NH2 )
a – asymmetric stretch; s – symmetric stretch, – stretch;  – bending; – rocking; ␥ – out of plane bending; W – wagging; D – butterfly mode; – swimming mode; – twist mode.
molecular systems. Mulliken charges are calculated by determining the electron population of each atom as defined in the basic functions [20]. The Mulliken charges calculated at different levels and at different basis sets are listed in Table 4. The graphical representation of the results has been given in Fig. 8. The charge distribution of 1,3 diglycinyl thiourea shows that the carbon atom attached with hydrogen atom is positive, whereas the remaining carbon atoms
are negatively charged. The nitrogen and oxygen atoms have negative charges whereas all the hydrogen atoms have positive charges. From these results, it will be possible to say that the charge distribution is not the same in basis set. The charges depending on basis set are due to polarization. The larger the polarization, the better the distribution. To explain this, the preferred position for nucleophilic attack has been identified. Further, it also gives the evidence for the
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Table 4 Mullikan charges of 1,3 diglycinyl thiourea. S. no
Atom
HF/6-31 G(d,p)
DFT/6-31 G(d,p)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
N C S N C N C O C N C O H H H H H H H H H H
−1.030677 1.242151 −0.519613 −1.147194 0.967673 −0.632771 0.283297 −0.599124 1.102007 −0.627044 0.288162 −0.734054 0.225412 0.437805 0.206797 0.208536 −0.001009 −0.003356 0.208572 0.261115 −0.048599 −0.088088
−1.247524 1.542803 −0.668381 −1.303063 1.125265 −0.737661 0.352635 −0.738378 1.32402 −0.687473 0.334894 −0.907996 0.269356 0.437678 0.242821 0.243586 0.003014 0.002929 0.232391 0.266765 −0.013096 −0.074585
1
2
3
4
5
6
7
8
9
10 11 12 13 14 15 16 17 18 19 20 21 22
N
C
S
N
C
N
C
O
C
N
C
O
H
H
H
H
H
H
H
H
H
H
2
1.5
HF/6-31G(d,p)
DFT/6-31G(d,p)
1
0.5
0
-0.5
-1
-1.5
Fig. 8. Graphical representation of Mullikan charges of 1,3 diglycinyl thiourea.
hydrogen bonding between O12 and H14 as the charges of these two atoms are higher when compared with other atoms in the molecule. 5. Conclusion Single crystals of 1,3 diglycinyl thiourea were grown from aqueous solutions by slow solvent evaporation method. The X-ray
diffraction analysis confirms that the crystal belongs to the monoclinic. Molecular geometry and optimized structure are compared with the reported values. Optical absorption studies show that the sample is optically transparent over wide wavelength region, no absorbance and good optical transmittance in the entire visible region. The FTIR analysis confirms the bonding interaction between glycine and thiourea molecule and compared them with those that are theoretically predicted. It is proved that there is good agreement between the observed values and the calculated values. A detailed insight about the electronic structure and charge distribution of the title compound has been discussed and reported. Acknowledgements The authors are thankful to SAIF, IIT, Madras, and VIT University for recording spectral data. References [1] N. Zhang, M.H. Jiang, D.R. Yuan, D. Xu, X.T. Tao, Z.S. Shao, J. Cryst. Growth 102 (1990) 581. [2] S.B. Monaco, L.E. Davis, S.P. Velsko, F.T. Wangand, D. Eimerl, J. Cryst. Growth 85 (1987) 252. [3] B. Uma Ramabadran, D.E. Zelmon, G.C. Kennedy, Appl. Phys. Lett. 60 (1992) 2589. [4] H.O. Marcy, L.F. Warren, M.S. Webb, C.A. Ebbers, S.P. Velsko, G.C. Kennedy, G.C. Catella, Appl. Opt. 31 (1992) 5051. [5] Z. Kotler, R. Hierle, D. Josse, J. Zyss, R. Masse, J. Opt. Soc. Am. B 9 (1992) 534. [6] N. Horiuchi, F. Lefaucheux, A. Ibanez, D. Josse, J. Zyss, Opt. Mater. 12 (1999) 351. [7] V. Venkataramanan, C.K. Subramanian, H.L. Bhat, J. Appl. Phys. 77 (1995) 6049. [8] L.F. Warren, R.E. Allred, R.J. Martinez, K.B. Wischmann (Eds.), Proceedings of the Fourth International Sample Electronics Conference, vol. 4, Society for the Advancement of Material and Process Engineering, Covina, CA, 1990, p. 388. [9] T.Y. Chang, D.E. Copper, G.L. Burdge, P. Polak, C.K. Lowe-Ma, C.Y. Chiang, C.K. Chaikan, D.O. Cowan (Eds.), Advanced Organic Solid Sate Materials, Materials Research Society Symposium Proceedings, vol. 173, Materials Research Society, Pittsburg, PA, 1990, p. 557. [10] R. Ezhil Vizhi, S. Kalainathan, Mater. Lett. 62 (2008) 791–794. [11] C. Kemnitz, Chemoffice Ultra 10. Trial Version, 2002. [12] M.J. Frisch, Gaussian 03, 2004. [13] A.D. Becke, Phys. Rev. A 38 (1988) 3098–3100. [14] N.R. Dhumane, S.S. Hussaini, V.V. Nawarkhele, M.D. Shirsat, Cryst. Res. Technol. 41 (2006) 897–901. [15] J. Ramajothi, S. Dhanushkodi, K. Nagarajan, Cryst. Res. Technol. 39 (2004) 414–420. [16] W. Lasocha, K. Lewinski, J. Appl. Crystallogr. 27 (1994) 437. [17] Y. Le Fur, R. Masse, M.Z. Cherkaoui, J.F. Nicoud, Z. Kristallogr. 210 (1995) 856. [18] R.M. Silverstein, G. Clayton Basseler, T.C. Morrill, Spectrometric Identification of Organic Compounds, V ed., John Wiley and Sons, Inc, New York, 1998. [19] R.H. Petrucci, W.S. Harwood, F.G. Herring, General Chemistry: Principles & Modern Applications, ninth ed., Pearson Education Inc, New Jersey, 2007. [20] S. Gunasekaran, S. Kumaresan, R. Arun Balaji, G. Anand, S. Srinivasan, J. Chem. Sci. 120 (May (3)) (2008) 315–324.
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Optik journal homepage: www.elsevier.de/ijleo
Synthesis, growth, molecular structure and spectral studies of 1,3 diglycinyl thiourea by density functional method M. Kumar a , R. Kanagadurai b , G. Mani a , S. Gunasekaran c , S. Kumaresan a,∗ a b c
PG and Research Department of Physics, Arignar Anna Government Arts College, Cheyyar 604 407, India PG and Research Department of Physics, Presidency College, Chennai 600 005, India St. Peter’s University, Avadi, Chennai 600 109, India
a r t i c l e
i n f o
Article history: Received 19 February 2014 Accepted 4 March 2015 Keywords: 1,3 Diglycinyl thiourea Hydrogen bonding FTIR UV DFT
a b s t r a c t Glycine is an important amino acid for building up protein synthesis and thiourea – a matrix metal multiplier combines to form a hybrid single crystal. Crystals of 1,3 diglycinyl thiourea were grown from aqueous solution by slow evaporation method. Powder X-ray diffraction analysis confirms that 1,3 diglycinyl thiourea crystallizes to monoclinic system. It is predicted that the molecular structure of 1,3 diglycinyl thiourea having well-defined bonding between C O. . .H and N H. . .O bond with a distance of 1.946 A˚ through hydrogen bonding. The structure and spectroscopic data of the molecule in the ground state have been calculated using ab initio Hartree Fock (HF) and density functional theory (DFT) (B3LYP) methods by employing 6-31 G(d,p) basis sets. Optical absorption study reveals that the transparency of the crystal in the entire visible region and the cutoff wavelength was found to be 236 nm. Mullikan population analyses on atomic charges analysis and molecular electrostatic potential and total density distribution are constructed to understand the electronic properties. The detailed interpretation of the vibrational spectra has been made on the basis of normal coordinate analysis. It is reported that there is a good agreement between theoretical and observed values. © 2015 Elsevier GmbH. All rights reserved.
1. Introduction The need for materials which combine large non linear optical characteristics with resistance to physical and chemical attack and good growth properties has led to the investigation of the semi organic materials. Semi organics are formed by combining organic molecules of high polarizability with mechanically strong and thermally stable inorganic molecules. The search for novel materials gaining increased attention in recent years and a wide variety of both organic and inorganic materials has been developed. Problems with both classes of materials have resulted in the investigation of semi organics [1–6]. The semi organic materials have the potentials for combining the high optical non linearity and chemical flexibility of organics with thermal stabilities and excellent transmittance of inorganic [7,8]. In search of these semi organic materials, urea and urea analogs have been explored [9]. 1,3 Diglycinyl thiourea single crystals were grown and characterized by XRD, optical and thermal properties were reported [10]. However, the detailed ab initio HF and B3LYP comparative studies on the complete FTIR spectrum and UV–vis spectrum of 1,3 diglycinyl thiourea have not
∗ Corresponding author. Tel.: +91 4182 22 5313. E-mail address: [email protected] (S. Kumaresan). http://dx.doi.org/10.1016/j.ijleo.2015.03.019 0030-4026/© 2015 Elsevier GmbH. All rights reserved.
been reported so far. Therefore, in the present study, molecular geometry, optimized parameters and vibrational frequencies are computed and the performances of the computational methods for HF and DFT (B3LYP) levels at 6-31 G(d,p) basis sets is compared. In this study, density functional theory (DFT/B3LYP) and by using hybrid functional, ab initio Hartree–Fock (HF) computations of the vibrational spectrum, the molecular geometry, and atomic charges calculations were carried out for 1,3 diglycinyl thiourea molecule. The experimental geometric data of the molecule were taken from the Cambridge crystallographic database [11]. The entire calculations were performed using ab initio HF and density functional theory (DFT) to support our wave number assignment. Density functional calculations are reported to provide excellent vibrational wave number of organic compounds if the calculated frequencies are scaled to compensate for the approximate treatment of electron correlation for basis set deficiencies and for the anharmonicity. 2. Experimental 2.1. Synthesis Glycine (AR) grade and thiourea (AR) were taken in the ratio 2:1 in distilled water and stirred in a magnetic stirrer for 6 h at room temperature. The solution was heated in steps of 5 ◦ C and
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M. Kumar et al. / Optik 126 (2015) 1117–1122 55 Glycine 50
Thiourea
Concentraon (gm/100ml)
1,3 diglycinyl thiourea 45
40
35
30
25
20 25
30
35
40
45
50
55
Temperatureºc
Fig. 1. Solubility curves for glycine, thiourea and 1,3 diglycinyl thiourea.
the precipitates if any to get dissolved. The solution is filtered and refluxed for homogeneity and purity. The obtained product is 1,3 diglycinyl thiourea.
Fig. 2. Photograph of a grown 1,3 diglycinyl thiourea single crystal.
2(NH2 CH2 COOH) + CS(NH2 )2 → C5 H10 N4 O2 S 2.2. Solubility test Solubility of 1,3 diglycinyl thiourea has been determined for five different temperatures at 30 ◦ C, 35 ◦ C, 40 ◦ C, 45 ◦ C and 50 ◦ C. Re-crystallized salt is used for this purpose. A 250 ml glass beaker containing 100 ml of deionized water was placed in the temperature bath. The initial temperature of the bath was set at 30 ◦ C. The beaker was closed with a sheet and placed in the magnetic stirrer. The synthesized salt was added in small amount and the stirring of the solution was continued till the formation of precipitate, which confirmed the saturation of the solution. The stirring further confirmed to have uniform temperature and concentration throughout the entire volume of the solution. On reaching the saturation, the equilibrium concentration of the solution was analyzed gravimetrically. The same procedure was followed for glycine and thiourea. Fig. 1 shows the solubility curves of glycine, thiourea and 1,3 diglycinyl thiourea. 2.3. Growth of 1,3 diglycinyl thiourea single crystals Single crystals of 1,3 diglycinyl thiourea were grown by slow evaporation technique at room temperature. Saturated solutions were prepared using re-crystallized salt at room temperature. The solutions were filtered using filter paper and kept undisturbed at room temperature and allow evaporating the solvent by covering a perforated thin mica sheet over the beaker. Transparent and optically good quality seeds were selected for the growth experiments. The period of growth ranged between 3 and 4 weeks and the harvested crystals are characterized. The photograph of optically transparent 1,3 diglycinyl thiourea single crystals are shown in Fig. 2.
Fig. 3. The optimized structure of 1,3 diglycinyl thiourea at DFT/6-31 G(d,p).
vibrational frequency calculations at the HF and DFT levels to characterize all stationary points as minima. The ground state optimized structural parameters such as bond length, bond angle and dihedral angle in various basis sets are presented in Table 1. From the theoretical values, it is found that some of the calculated parameters are slightly deviated from the experimental values, due to the fact that theoretical calculations belong to molecule in the gaseous phase and the experimental results belong to molecule in solid state. In this work, we performed full geometry optimization of the title compound. The optimized structure of title compound at DFT is shown in Fig. 3. The B3LYP method leads to geometry parameters, which are close to experimental data. A statistical treatment of these data shows that for the bond lengths B3LYP/631 G(d,p) are slightly better than the HF/6-31 G(d,p) geometry. The slight variation with the experimental value is due to the fact that the optimization performed in an isolated condition, whereas the experimental environment affected the X-ray structure.
3. Theoretical methods 3.2. Vibrational spectra 3.1. Molecular geometry The entire calculations were performed at ab initio HF and DFT (B3LYP) levels at 6-31 G(d,p) basis sets on a Pentium V/1.6 GHz personal computer using Gaussian 03W program package [12] and applying geometry optimization [13]. Initial geometry generated was minimized at the Hartree–Fock levels using 6-31 G(d,p) basis set and again re-optimized at DFT (B3LYP) levels at 6-31 G(d,p) basis sets. The optimized structural parameters were used in the
The present molecule has C1 symmetry and has 60 normal modes of vibrations; all the fundamental modes are active in infrared. None of the predicted vibrational spectra have any imaginary frequency, implying that the optimized geometry is located at the local lowest point on the potential energy surface. We know that, ab initio Hartree–Fock and DFT potentials systematically overestimate the vibrational wave numbers. These discrepancies corrected wither by computing harmonic corrections explicitly or
M. Kumar et al. / Optik 126 (2015) 1117–1122
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Table 1 Optimized geometric parameters of 1,3 diglycinyl thiourea at HF and DFT (B3LYP) levels of 6-31 G (d,p) basis sets. Theoretical
Experimental
HF/6-31 G(d,p) R(1-2) R(1-9) R(1-13) R(2-3) R(2-4) R(4-5) R(4-14) R(5-7) R(5-8) R(6-7) R(6-15) R(6-16) R(7-17) R(7-18) R(9-11) R(9-12) R(10-11) R(10-19) R(10-20) R(11-21) R(11-22) R(12-14)
B3LYP/6-31 G(d,p) 1.39 1.37 1 1.71 1.35 1.39 1.01 1.52 1.21 1.44 0.99 0.99 1.08 1.08 1.51 1.22 1.43 0.99 0.99 1.08 1.09 1.95
A(2-1-9) A(2-1-13) A(1-2-3) A(1-2-4) A(9-1-13) A(1-9-11) A(1-9-12) A(3-2-4) A(2-4-5) A(2-4-14) A(5-4-14) A(4-5-7) A(4-5-8) A(4-14-12) A(7-5-8) A(5-7-6) A(5-7-17) A(5-7-18) A(7-6-15) A(7-6-16) A(6-7-17) A(6-7-18) A(15-6-16) A(17-7-18) A(11-9-12) A(9-11-10) A(9-11-21) A(9-11-22) A(9-12-14) A(11-10-19) A(11-10-20) A(10-11-21) A(10-11-22) A(19-10-20) A(21-11-22)
130.86 111.77 116.4 115.37 117.38 114.63 123.33 128.22 128.77 118.4 112.83 113.87 126.05 131.66 120.08 114.52 106.26 106.21 118.76 118.76 111.54 111.6 114.65 106.18 121.99 109.81 109.35 106.24 100.32 117.62 116.82 110.04 114.38 116.3 106.86
R(1-2) R(1-9) R(1-13) R(2-3) R(2-4) R(4-5) R(4-14) R(5-7) R(5-8) R(6-7) R(6-15) R(6-16) R(7-17) R(7-18) R(9-11) R(9-12) R(10-11) R(10-19) R(10-20) R(11-21) R(11-22) R(12-14)
1.411 1.383 1.014 1.709 1.366 1.401 1.035 1.54 1.235 1.451 1.008 1.008 1.097 1.097 1.524 1.251 1.442 1.007 1.01 1.102 1.109 1.946
by introducing a scaled field or directly scaling the calculated wave number with the proper factor. The DFT method is superior to HF and semi-empirical methods in terms of realistic reproduction of both band intensity distribution and general spectral features.
X-ray data/ref. [11] A(2-1-9) A(2-1-13) A(1-2-3) A(1-2-4) A(9-1-13) A(1-9-11) A(1-9-12) A(3-2-4) A(2-4-5) A(2-4-14) A(5-4-14) A(4-5-7) A(4-5-8) A(4-14-12) A(7-5-8) A(5-7-6) A(5-7-17) A(5-7-18) A(7-6-15) A(7-6-16) A(6-7-17) A(6-7-18) A(15-6-16) A(17-7-18) A(11-9-12) A(9-11-10) A(9-11-21) A(9-11-22) A(9-12-14) A(11-10-19) A(11-10-20) A(10-11-21) A(10-11-22) A(19-10-20) A(21-11-22)
130.5 111.5 116.9 114.9 117.9 114.6 123.5 128.2 128.4 119.4 112.2 112.2 126.6 130.8 121.2 114.1 106.4 106.4 118.3 118.2 111.6 111.9 114.2 106 121.8 109.6 108.5 106.4 100.8 117.7 115.1 111.8 114.2 116.3 106
R(1-2) R(1-9) R(1-13) R(2-3) R(2-4) R(4-5) R(4-14) R(5-7) R(5-8) R(6-7) R(6-15) R(6-16) R(7-17) R(7-18) R(9-11) R(9-12) R(10-11) R(10-19) R(10-20) R(11-21) R(11-22)
1.369 1.369 1.012 1.576 1.369 1.369 1.012 1.509 1.208 1.468 1.02 1.02 1.113 1.113 1.509 1.208 1.468 1.02 1.02 1.113 1.113
A(2-1-9) A(2-1-13) A(1-2-3) A(1-2-4) A(9-1-13) A(1-9-11) A(1-9-12) A(3-2-4) A(2-4-5) A(2-4-14) A(5-4-14) A(4-5-7) A(4-5-8)
125.1 117.5 124.3 120 117.5 114.3 122.9 115.7 125.1 117.5 117.5 114.3 122.9
A(7-5-8) A(5-7-6) A(5-7-17) A(5-7-18) A(7-6-15) A(7-6-16) A(6-7-17) A(6-7-18) A(15-6-16) A(17-7-18) A(11-9-12) A(9-11-10) A(9-11-21) A(9-11-22)
122.8 110.7 108.8 108.8 109.5 109.5 108.8 108.8 104.5 110.9 122.8 110.7 108.8 108.8
A(11-10-19) A(11-10-20) A(10-11-21) A(10-11-22) A(19-10-20) A(21-11-22)
109.5 109.5 108.8 108.8 104.5 110.9
revealed that 1,3 diglycinyl thiourea crystal belongs to monoclinic crystal system. The obtained crystallographic data are presented in Table 2. 4.2. Optical absorption studies
4. Results and discussion 4.1. X-ray diffraction analysis The scheme of the crystal data from the Cambridge crystal data were presented in Table 2. From the table, it is observed that the ˚ c = 12.273 A˚ and cell parameters are a = 5.5753 A˚ and b = 5.994 A, V = 310.81 A˚ 3 . The crystals that belong to the monoclinic crystal system are in good agreement with the reported data [10] and are indexed. X-ray diffraction analysis was done using diffractometer model Philips Powder X-ray diffractometer using CuK␣ ˚ and is shown in Fig. 4. The samples were scanned ( = 1.5418 A) over the range 20–60◦ at a scan rate of 1◦ /min. The unit cell dimensions were calculated using PROSZKI software package. The study
The optical absorption spectrum of 1,3 diglycinyl thiourea single crystal was recorded in the range 200–800 nm using a Varian Cary 5E model spectrophotometer and is shown in Fig. 5. The spectrum shows that 1,3 diglycinyl thiourea crystal has good transmission in the entire region. The lower cutoff wavelength lies below 236 nm, whereas the calculated cutoff wavelength is at 258 nm at TD DFT/6-31 G(d,p) basis set. The overestimation of value in the theoretical spectra is due to anharmonicity in the real system. Efficient
Table 2 Crystal data of 1,3 diglycinyl thiourea single crystal. Crystallographic data
1,3 Diglycinyl thiourea
˚ a (A) ˚ b (A) ˚ c (A)
5.5753 5.994 12.273 310.81 90◦ 113◦ 90◦ Monoclinic
Volume (A˚ 3 ) ˛ ˇ Crystal system
Fig. 4. Powder XRD pattern of 1,3 diglycinyl thiourea.
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M. Kumar et al. / Optik 126 (2015) 1117–1122
236 nm, 1.267
1.2
Experimental
1.0 0.8 0.6
Absorbance
0.4 0.2 0.0 2.0
TD DFT/6-31G(d,p)
258 nm, 2.101
1.5
1.0
0.5
0.0
200
400
600
800
Wavelength (nm)
Fig. 7. The contour map of molecular electrostatic potential surface of 1,3 diglycinyl thiourea.
Fig. 5. The optical absorption spectrum of DGT crystal.
NLO crystals have an optical transparency lower cutoff wavelength between 200 and 400 nm [14]. From the UV–vis spectral analysis it is clear that the cut off wavelength is at 236 nm and there is no significant absorption in the UV region thereby confirming the advantages of the crystals, the large transmission in the entire region and short cutoff wavelength enable the crystals to be useful for second harmonic generation. The percentage of absorption of 1,3 diglycinyl thiourea crystals is more than one, indicating that these crystals have good optical property. 4.3. FTIR studies 1,3 Diglycinyl thiourea single crystal was subjected to the FTIR studies. The various functional groups present in 1,3 diglycinyl thiourea crystals were identified and confirmed by the FTIR study. The complete vibrational assignments of fundamental modes of 1,3 diglycinyl thiourea are presented in Table 3. The spectrum was recorded in the range 4000–400 cm−1 using BRUKER IFS – 66V spectrometer, by KBr pellet technique and is shown in Fig. 6.
DFT/6-31 G(d,p)
4.4. Vibrational assignments A medium sharp band at 1721 cm−1 is due to NH2 scissoring and the scaled value of 1722 in B3LYP/6-31 G(d,p) is assigned. A weak peak at 3441 cm−1 is assigned to NH2 asymmetric stretching and calculated the values at 3431 and 3450 in HF and DFT methods, respectively. The CN asymmetric and symmetric stretching vibrations are observed at 1089 and 1472 cm−1 , respectively. The CS asymmetric stretching vibration is observed at 1408 cm−1 . Thiourea could form metal complexes by coordinate bonds through sulfur or nitrogen. Thiourea exhibits characteristic peaks at 1627, 1472, 1417, 1089, 740 and 494 cm−1 [15]. The CS symmetric stretching is observed at 740 cm−1 . The band at 494 cm−1 is due to asymmetric NCN bending. If the bonding is through sulfur, there will be a decrease in the CS stretching frequency and an increase in the CN stretching frequency. The reverse happens if it is through nitrogen. The peak set around 921 and 894 cm−1 could be attributed to CH2 wagging and CNH and CNC out of plane banding. A peptide bond CO NH that is formed between the NH2 in glycine and thiourea is clearly visible in the spectrum between 1030 and 1750 cm−1 [16,17]. Also the C O and N H stretching vibrations of CO NH are visible at 2686 cm−1 and 2706 cm−1 in the stimulated spectra, whereas both the peaks absent in the experimental spectrum. The broad envelope positioned between 2750 and 3500 cm−1 corresponds to the symmetric and asymmetric stretching modes of NH2 group [18].
Transmittance (T%)
4.5. Molecular electrostatic potential mapping (MESP) studies Molecular electrostatic potential mapping helps to a larger extent in investigating the structure and the charge distribution of molecules three dimensionally with its physiochemical properties. The molecular electrostatic potential (MESP) of 1.3 diglycinyl thiourea is carried out using DFT/B3LYP/6-31 G(d,p) method and it visibly suggests that the hydrogen atoms attached to the ends of the molecular chain beat the maximum bang of positive charge [19]. The molecular electrostatic potential surface (MESP) provides a visual method to understand the polarity of the molecule. The purpose of finding the electrostatic potential is to find the reactive site of a molecule. The MESP mapped surface of the compound is shown in Fig. 7 and computed at 0.004 at iso-density surface.
HF/6-31 G(d,p)
Expe rimen tal
4000
3000
2000
1000
0
4.6. Mulliken charges
-1
Wavenu mber (cm ) Fig. 6. FTIR spectra of 1,3 diglycinyl thiourea.
The calculation of effective atomic charges plays an important role in the application of quantum mechanical calculations to
M. Kumar et al. / Optik 126 (2015) 1117–1122
1121
Table 3 Observed FTIR and calculated wave number for 1,3 diglycinyl thiourea using HF 6-31 G(d,p) and DFT/B3LYP G(d,p) methods. Theoretical
Experimental
B3LYP/6-31 G(d,p)
HF/6-31 G(d,p)
Unscaled
Scaled
IR intensity
Unscaled
Scaled
IR intensity
30 43 49 69 101 103 156 178 185 226 271 280 325 384 451 481 523 545 547 589 658 668 704 788 795 908 931 996 1038 1077 1117 1132 1161 1184 1193 1236 1254 1261 1362 1368 1397 1443 1502 1547 1554 1572 1664 1710 1719 1747 2920 2998 3057 3102 3239 3585 3596 3609 3726 3730
29 41 47 66 97 99 150 171 177 217 260 269 312 369 433 462 502 523 525 565 632 641 676 756 763 872 894 957 997 1034 1073 1087 1115 1137 1145 1187 1204 1210 1308 1313 1342 1385 1442 1486 1492 1509 1598 1642 1650 1677 2686 2758 2812 2854 2980 3298 3308 3320 3428 3431
1.38 4.20 1.86 10.41 3.94 9.61 30.28 10.59 4.14 3.02 4.22 1.46 26.99 13.73 98.65 217.00 243.99 46.41 46.11 29.66 7.83 46.64 12.47 103.04 35.38 7.12 20.77 12.94 1.50 126.53 15.56 36.07 105.27 4.84 57.01 76.31 68.31 82.80 342.25 5.88 95.50 61.59 6.90 526.07 244.42 568.00 144.62 46.09 41.18 81.68 61.58 44.60 18.47 8.70 302.49 28.00 16.00 11.44 17.47 20.80
27 40 58 69 108 125 184 203 212 246 281 305 351 405 487 537 578 587 604 643 717 724 766 835 891 985 1009 1078 1127 1154 1205 1211 1265 1291 1302 1342 1380 1397 1477 1488 1529 1592 1624 1666 1718 1768 1817 1845 1893 1936 3111 3223 3229 3270 3632 3833 3840 3852 3963 3966
26 38 55 66 103 120 176 195 204 236 269 293 337 389 467 515 555 564 580 617 688 695 735 802 856 946 968 1035 1082 1108 1157 1162 1214 1239 1250 1288 1325 1341 1418 1428 1468 1528 1559 1600 1649 1654 1659 1679 1722 1762 2706 2804 2810 2845 3160 3335 3341 3351 3447 3450
1.10 4.43 2.07 13.08 5.72 4.11 20.80 3.20 50.65 2.33 4.20 0.42 13.65 13.32 40.54 306.54 273.81 127.98 31.26 35.46 34.52 60.71 65.06 41.13 141.13 1.89 11.65 7.31 10.05 221.71 52.03 14.75 85.51 199.85 8.91 88.23 249.60 42.80 560.27 3.64 52.87 31.35 3.43 13.70 598.34 758.53 75.95 64.64 150.22 125.65 49.52 15.65 25.62 8.14 305.07 15.36 20.98 65.78 32.93 33.30
Vibrational assignment
FTIR
Intensity
Wave number (cm−1 )
%
509
82
673 731
91 84
894 921
79 96
1030
97
1111
95
1328 1408 1433 1483
75 64 94 80
1618
48
1721
3213
48
3441
27
Lattice vibrations Lattice vibrations Lattice vibrations Lattice vibrations Lattice distortion Lattice distortion W(NH2 + C NH2 ) W(NH2 + C CH2 ) W(NH2 + C NH2 ) Lattice distortion D(C NH2 ) Lattice twist Lattice twist (CO· · ·H + NH· · ·O) (CO· · ·H) + (CCH) (CO· · ·H + CNC) (C NH2 ) (C NH2 ) (C NH2 ) + (C CH2 ) Lattice breath (C NH2 ) + (C NH· · ·O) (CS) + (C NH· · ·O) + ␥(CNH) (C CH2 + C NH2 ) + ␥(CCO + NCO) (CS) + W(CH2 ) + ␥(CNC + CNH) (C NH· · ·O) ␥(C NH2 ) + (CNH) + (CH2 ) W(CH2 ) + ␥(CNC + CNH) ␥(CNC + CNH + NCO) ␥(CCO + NHO) ␥(NH· · ·O + CO· · ·H) ␥(CNC + CNH + CO· · ·H) ␥(C NH2 ) + (CNH) ␥(C NH2 ) + (CNH) W(NH2 + CH2 ) W(CH2 ) + ␥(CNC + CNH) ␥(CNC + CNH + NCO) ␥(CNC + CNH + NCO) (C CH2 + C NH2 + CCO + NCO) (CH2 ) + (CNH) (CNC + CNH + NCO + NH· · ·O) (CH2 + NH2 ) cradle a (CS) + (CH2 ) (C CH2 ) + NH2 cradle CH2 scissoring (C CH2 + CNH + NHO) (C CH2 + CNH + COH + NHO) (COH + NHO) NH2 scissoring NH2 scissoring (CO) + (NH2 ) + (COH) + (CC NH2 ) (CO) + (NH2 ) + (COH) (CH) (CH) s (CH2 ) a (CH2 ) (NH) s (NH2 ) s (NH2 ) a (NH2 ) a (NH2 )
a – asymmetric stretch; s – symmetric stretch, – stretch;  – bending; – rocking; ␥ – out of plane bending; W – wagging; D – butterfly mode; – swimming mode; – twist mode.
molecular systems. Mulliken charges are calculated by determining the electron population of each atom as defined in the basic functions [20]. The Mulliken charges calculated at different levels and at different basis sets are listed in Table 4. The graphical representation of the results has been given in Fig. 8. The charge distribution of 1,3 diglycinyl thiourea shows that the carbon atom attached with hydrogen atom is positive, whereas the remaining carbon atoms
are negatively charged. The nitrogen and oxygen atoms have negative charges whereas all the hydrogen atoms have positive charges. From these results, it will be possible to say that the charge distribution is not the same in basis set. The charges depending on basis set are due to polarization. The larger the polarization, the better the distribution. To explain this, the preferred position for nucleophilic attack has been identified. Further, it also gives the evidence for the
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M. Kumar et al. / Optik 126 (2015) 1117–1122
Table 4 Mullikan charges of 1,3 diglycinyl thiourea. S. no
Atom
HF/6-31 G(d,p)
DFT/6-31 G(d,p)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
N C S N C N C O C N C O H H H H H H H H H H
−1.030677 1.242151 −0.519613 −1.147194 0.967673 −0.632771 0.283297 −0.599124 1.102007 −0.627044 0.288162 −0.734054 0.225412 0.437805 0.206797 0.208536 −0.001009 −0.003356 0.208572 0.261115 −0.048599 −0.088088
−1.247524 1.542803 −0.668381 −1.303063 1.125265 −0.737661 0.352635 −0.738378 1.32402 −0.687473 0.334894 −0.907996 0.269356 0.437678 0.242821 0.243586 0.003014 0.002929 0.232391 0.266765 −0.013096 −0.074585
1
2
3
4
5
6
7
8
9
10 11 12 13 14 15 16 17 18 19 20 21 22
N
C
S
N
C
N
C
O
C
N
C
O
H
H
H
H
H
H
H
H
H
H
2
1.5
HF/6-31G(d,p)
DFT/6-31G(d,p)
1
0.5
0
-0.5
-1
-1.5
Fig. 8. Graphical representation of Mullikan charges of 1,3 diglycinyl thiourea.
hydrogen bonding between O12 and H14 as the charges of these two atoms are higher when compared with other atoms in the molecule. 5. Conclusion Single crystals of 1,3 diglycinyl thiourea were grown from aqueous solutions by slow solvent evaporation method. The X-ray
diffraction analysis confirms that the crystal belongs to the monoclinic. Molecular geometry and optimized structure are compared with the reported values. Optical absorption studies show that the sample is optically transparent over wide wavelength region, no absorbance and good optical transmittance in the entire visible region. The FTIR analysis confirms the bonding interaction between glycine and thiourea molecule and compared them with those that are theoretically predicted. It is proved that there is good agreement between the observed values and the calculated values. A detailed insight about the electronic structure and charge distribution of the title compound has been discussed and reported. Acknowledgements The authors are thankful to SAIF, IIT, Madras, and VIT University for recording spectral data. References [1] N. Zhang, M.H. Jiang, D.R. Yuan, D. Xu, X.T. Tao, Z.S. Shao, J. Cryst. Growth 102 (1990) 581. [2] S.B. Monaco, L.E. Davis, S.P. Velsko, F.T. Wangand, D. Eimerl, J. Cryst. Growth 85 (1987) 252. [3] B. Uma Ramabadran, D.E. Zelmon, G.C. Kennedy, Appl. Phys. Lett. 60 (1992) 2589. [4] H.O. Marcy, L.F. Warren, M.S. Webb, C.A. Ebbers, S.P. Velsko, G.C. Kennedy, G.C. Catella, Appl. Opt. 31 (1992) 5051. [5] Z. Kotler, R. Hierle, D. Josse, J. Zyss, R. Masse, J. Opt. Soc. Am. B 9 (1992) 534. [6] N. Horiuchi, F. Lefaucheux, A. Ibanez, D. Josse, J. Zyss, Opt. Mater. 12 (1999) 351. [7] V. Venkataramanan, C.K. Subramanian, H.L. Bhat, J. Appl. Phys. 77 (1995) 6049. [8] L.F. Warren, R.E. Allred, R.J. Martinez, K.B. Wischmann (Eds.), Proceedings of the Fourth International Sample Electronics Conference, vol. 4, Society for the Advancement of Material and Process Engineering, Covina, CA, 1990, p. 388. [9] T.Y. Chang, D.E. Copper, G.L. Burdge, P. Polak, C.K. Lowe-Ma, C.Y. Chiang, C.K. Chaikan, D.O. Cowan (Eds.), Advanced Organic Solid Sate Materials, Materials Research Society Symposium Proceedings, vol. 173, Materials Research Society, Pittsburg, PA, 1990, p. 557. [10] R. Ezhil Vizhi, S. Kalainathan, Mater. Lett. 62 (2008) 791–794. [11] C. Kemnitz, Chemoffice Ultra 10. Trial Version, 2002. [12] M.J. Frisch, Gaussian 03, 2004. [13] A.D. Becke, Phys. Rev. A 38 (1988) 3098–3100. [14] N.R. Dhumane, S.S. Hussaini, V.V. Nawarkhele, M.D. Shirsat, Cryst. Res. Technol. 41 (2006) 897–901. [15] J. Ramajothi, S. Dhanushkodi, K. Nagarajan, Cryst. Res. Technol. 39 (2004) 414–420. [16] W. Lasocha, K. Lewinski, J. Appl. Crystallogr. 27 (1994) 437. [17] Y. Le Fur, R. Masse, M.Z. Cherkaoui, J.F. Nicoud, Z. Kristallogr. 210 (1995) 856. [18] R.M. Silverstein, G. Clayton Basseler, T.C. Morrill, Spectrometric Identification of Organic Compounds, V ed., John Wiley and Sons, Inc, New York, 1998. [19] R.H. Petrucci, W.S. Harwood, F.G. Herring, General Chemistry: Principles & Modern Applications, ninth ed., Pearson Education Inc, New Jersey, 2007. [20] S. Gunasekaran, S. Kumaresan, R. Arun Balaji, G. Anand, S. Srinivasan, J. Chem. Sci. 120 (May (3)) (2008) 315–324.